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/tool-data/bfast_indexes.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/
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  1. #This is a sample file distributed with Galaxy that enables tools
    2. 

  2. #to use a directory of BFAST indexed sequences data files.  You will need
    3. 

  3. #to create these data files and then create a bfast_indices.loc file 
    4. 

  4. #similar to this one (store it in this directory) that points to 
    5. 

  5. #the directories in which those files are stored. The bfast_indexes.loc 
    6. 

  6. #file has this format (white space characters are TAB characters):
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  7. #
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  8. #<unique_id>	<build>	<galaxy format extensions valid1,valid2>	<description>	<bfast_index_directory>
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  9. #
    10. 

  10. #
    11. 

  11. #So, for example, if you had hg18 indexed for 40+ bp NT reads stored in 
    12. 

  12. #/galaxy/data/hg18/bfast_index/nt/40+, 
    13. 

  13. #then the bfast_indices.loc entry could look like this:
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  14. #
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  15. #hg18_nt_40+	hg18	fastqsanger	hg18: 40+ bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
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  16. #
    17. 

  17. #and your /depot/data2/galaxy/hg18/bfast/nt/40+ directory
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  18. #would contain hg18.fa.*.brg and hg18.fa.*.bif files:
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  19. #hg18.fa.nt.brg
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  20. #hg18.fa.nt.1.1.bif
    21. 

  21. #hg18.fa.nt.2.1.bif
    22. 

  22. #...etc...
    23. 

  23. #or similarly for color space indexes:
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  24. #hg18.fa.nt.brg #NB: the localalign process requires the nucleotide brg file
    25. 

  25. #hg18.fa.cs.brg
    26. 

  26. #hg18.fa.cs.1.1.bif
    27. 

  27. #hg18.fa.cs.2.1.bif
    28. 

  28. #...etc...
    29. 

  29. #
    30. 

  30. #a 'generic' directory can be used to hold intermixed NT and CS indexes, when differentiating is not needed, the bfast_indices.loc entry could look like this:
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  31. #hg18_standard	hg18	fastqsanger,fastqcssanger	hg18 standard indexes	/galaxy/data/hg18/bfast_index/hg18.fa
    32. 

  32. #
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  33. #The use of symlinks to prevent copying of e.g. .fa and .brg files is recommended
    34. 

  34. #
    35. 

  35. #hg18_nt_40+	hg18	fastqsanger	hg18: 40+ bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
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  36. #hg18_cs_50+	hg18	fastqcssanger	hg18: 50+ bp Color space reads	/galaxy/data/hg18/bfast_index/cs/50+/hg18.fa
    37. 

  37. #hg18_nt_40-	hg18	fastqsanger	hg18: 40- bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40-/hg18.fa
    38. 

  38. #phiX_nt_50	phiX	fastqsanger	phiX: 50 bp NT Space reads	/galaxy/data/phiX/bfast_index/nt/50/phiX.fa
    39. 

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